Mercurial > repos > galaxyp > peptideshaker
comparison searchgui.xml @ 56:1beff3ddce58 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75"
| author | galaxyp |
|---|---|
| date | Wed, 20 Jan 2021 13:29:07 +0000 |
| parents | bb0130ff73ce |
| children | da885ca16cb2 |
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| 55:bb0130ff73ce | 56:1beff3ddce58 |
|---|---|
| 20 #set $temp_stderr = "searchgui_stderr" | 20 #set $temp_stderr = "searchgui_stderr" |
| 21 #set $bin_dir = "bin" | 21 #set $bin_dir = "bin" |
| 22 | 22 |
| 23 mkdir output; | 23 mkdir output; |
| 24 mkdir output_reports; | 24 mkdir output_reports; |
| 25 mkdir temp_folder; | |
| 26 mkdir log_folder; | |
| 25 cwd=`pwd`; | 27 cwd=`pwd`; |
| 26 export HOME=\$cwd; | 28 export HOME=\$cwd; |
| 27 | 29 |
| 28 echo "" > $temp_stderr && | 30 echo "" > $temp_stderr && |
| 29 | 31 |
| 61 --exec_dir="\$cwd/${bin_dir}" | 63 --exec_dir="\$cwd/${bin_dir}" |
| 62 -spectrum_files \$cwd | 64 -spectrum_files \$cwd |
| 63 -fasta_file "\$cwd/input_fasta_file.fasta" | 65 -fasta_file "\$cwd/input_fasta_file.fasta" |
| 64 -output_folder \$cwd/output | 66 -output_folder \$cwd/output |
| 65 -id_params ./SEARCHGUI_IdentificationParameters.par | 67 -id_params ./SEARCHGUI_IdentificationParameters.par |
| 66 | 68 -temp_folder \$cwd/temp_folder |
| 69 -log \$cwd/log_folder | |
| 67 -threads "\${GALAXY_SLOTS:-12}" | 70 -threads "\${GALAXY_SLOTS:-12}" |
| 68 | 71 |
| 69 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' | 72 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' |
| 70 -correct_titles "${searchgui_advanced.correct_titles}" | 73 -correct_titles "${searchgui_advanced.correct_titles}" |
| 71 $searchgui_advanced.missing_titles | 74 $searchgui_advanced.missing_titles |